forked from nfdi4plants/nfdi4plants_ontology
-
Notifications
You must be signed in to change notification settings - Fork 0
/
nfdi4pso.obo.obsolete
2411 lines (2124 loc) · 84.1 KB
/
nfdi4pso.obo.obsolete
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
format-version: 1.2
data-version: init/2020-12-01
saved-by: muehlhaus
default-namespace: NFDI4PSO
remark: This ontology is obsolete and has been replaced with dpbo.obo
remark: coverage: Missing Terms for the DataPLANT end-point repository templates
remark: creator: Dominik Brilhaus <dominik.brilhaus<-at->hhu.de>
remark: creator: Hajira Jabeen <hajira.jabeen<-at->uni-koeln.de>
ontology: nfdi4pso
property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0001-9021-3197 xsd:string
property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0003-1476-2121 xsd:string
property_value: http://purl.org/dc/elements/1.1/title "The DataPlant Ontology" xsd:string
owl-axioms: Prefix(owl:=<http://www.w3.org/2002/07/owl#>)\nPrefix(rdf:=<http://www.w3.org/1999/02/22-rdf-syntax-ns#>)\nPrefix(xml:=<http://www.w3.org/XML/1998/namespace>)\nPrefix(xsd:=<http://www.w3.org/2001/XMLSchema#>)\nPrefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)\n\n\nOntology(\nDeclaration(AnnotationProperty(<http://purl.obolibrary.org/obo/IAO_0000115>))\n\n\nAnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/NFDI4PSO_1000119> \"\"^^xsd:string)\nAnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/NFDI4PSO_1000120> \"\"^^xsd:string)\nAnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/NFDI4PSO_1000126> \"\"^^xsd:string)\n)
treat-xrefs-as-equivalent: OBI
treat-xrefs-as-equivalent: EFO
treat-xrefs-as-equivalent: GENEPIO
treat-xrefs-as-equivalent: CHMO
treat-xrefs-as-equivalent: NCIT
treat-xrefs-as-equivalent: PSO
treat-xrefs-as-equivalent: CHEBI
treat-xrefs-as-equivalent: SIO
treat-xrefs-as-equivalent: ENVO
treat-xrefs-as-equivalent: ERO
treat-xrefs-as-equivalent: MS
treat-xrefs-as-equivalent: PATO
treat-xrefs-as-equivalent: UO
treat-xrefs-as-equivalent: OME
treat-xrefs-as-equivalent: EDAM
treat-xrefs-as-equivalent: dc
treat-xrefs-as-equivalent: SCTID
[Term]
id: NFDI4PSO:0000001
name: growth plot design
def: "A plan specification that states how treatments are allocated to the experimental units. It refers to the conceptual framework within which the experiment is conducted" []
synonym: "Experimental Randomisation" RELATED []
disjoint_from: NFDI4PSO:0000002 ! Read Alignment Software
is_obsolete: true
[Term]
id: NFDI4PSO:0000002
name: Read Alignment Software
def: "The software used for read alignment i.e http://edamontology.org/operation_3198 or http://purl.obolibrary.org/obo/OBI_0002478" []
comment: “We might need to add the relationship with the class referenced above”
is_obsolete: true
[Term]
id: NFDI4PSO:0000003
name: Read Alignment Software Version
def: "The version of the read alignment software (NFDI4PSO:0000002)." []
is_obsolete: true
[Term]
id: NFDI4PSO:0000004
name: Read Alignment Software Parameters
def: "The parameters of the read alignment software (NFDI4PSO:0000002)." []
is_obsolete: true
[Term]
id: NFDI4PSO:0000005
name: Humidity Day
def: "This term defines the relative humidity of the air at daytime, it is a specialised concept of http://purl.obolibrary.org/obo/PECO_0007197" []
comment: "is_a: http://purl.obolibrary.org/obo/PECO_0007197"
is_obsolete: true
[Term]
id: NFDI4PSO:0000006
name: Humidity Night
def: "This term defines the relative humidity of the air at nighttime, it is a specialised concept of http://purl.obolibrary.org/obo/PECO_0007197”" []
comment: "is_a: http://purl.obolibrary.org/obo/PECO_0007197"
is_obsolete: true
[Term]
id: NFDI4PSO:0000007
name: Temperature Day
def: "This term defines the air temperature at daytime, it is a specialised concept of http://purl.obolibrary.org/obo/ENVO_09200001" []
comment: “is_a: http://purl.obolibrary.org/obo/ENVO_09200001”
is_obsolete: true
[Term]
id: NFDI4PSO:0000008
name: Temperature Night
def: "This term defines the air temperature at nighttime, it is a specialised concept of http://purl.obolibrary.org/obo/ENVO_09200001”" []
comment: “is_a: http://purl.obolibrary.org/obo/ENVO_09200001”
is_obsolete: true
[Term]
id: NFDI4PSO:0000009
name: Sample Collection Method
def: "Details of method to gather (e.g. scissors, scalpel) or pool the sample, tissue, organ”" []
is_obsolete: true
[Term]
id: NFDI4PSO:0000010
name: Metabolism quenching method
def: "Method used to stop the metabolism in the sample (e.g. shock-freeze in liquid nitrogen). May include the time passed since sample collection.”" []
comment: “”
is_obsolete: true
[Term]
id: NFDI4PSO:0000011
name: Sample storage
def: "The method used for sample storage. Should include the temperature of the sample. May include the medium (freezer or liquid nitrogen) and/or additional processing (freeze-drying) of the sample”" []
comment: “”
is_obsolete: true
[Term]
id: NFDI4PSO:0000012
name: Bio entity
def: "The biological entity (e.g. RNA, DNA, metabolites, proteins, lipids) to be extracted from a biosource targeted for assay / measurement.”" []
comment: “”
is_obsolete: true
[Term]
id: NFDI4PSO:0000013
name: Biosource amount
def: "The amount (typically in milligram) of material from which a bio entity (NFDI4PSO:0000012) is extracted.”" []
comment: “”
is_obsolete: true
[Term]
id: NFDI4PSO:0000014
name: Extraction Kit
def: "The name of the commercial kit used for extraction of a bio entity (NFDI4PSO:0000012). Should include the company name.”" []
comment: “”
is_obsolete: true
[Term]
id: NFDI4PSO:0000015
name: Library layout
def: "Determines the choice of DNA sequencing strategy, in which a single read is initiated from each end (paired-end) or one end (single-end) of DNA fragment”" []
comment: “Adapted from http://purl.obolibrary.org/obo/NCIT_C150423"
is_obsolete: true
[Term]
id: NFDI4PSO:0000016
name: Library RNA amount
def: "Amount of RNA (typically microgram) used as starting material for library construction (http://purl.obolibrary.org/obo/GENEPIO_0001994)”" []
comment: “”
is_obsolete: true
[Term]
id: NFDI4PSO:0000017
name: Base-calling Software
def: "The name of the software used for base-calling." []
comment: Alternative: http://edamontology.org/operation_3185
xref: EDAM:operation_3185
is_obsolete: true
[Term]
id: NFDI4PSO:0000018
name: Base-calling Software Version
def: "The version of the Base-calling Software (NFDI4PSO:0000017).”" []
comment: “”
is_obsolete: true
[Term]
id: NFDI4PSO:0000019
name: Base-calling Software Parameters
def: "The parameters of the Base-calling Software (NFDI4PSO:0000017).”" []
comment: “”
is_obsolete: true
[Term]
id: NFDI4PSO:0000020
name: Library strand
def: "Determines the read direction. Only applies to nucleotide sequencing in paired-end layout (NFDI4PSO:0000015)”" []
comment: “”
is_obsolete: true
[Term]
id: NFDI4PSO:0000021
name: Raw data file format
def: "File format of the raw data file”" []
comment: “This is a specialization of https://ifb-elixirfr.github.io/edam-browser/#http://edamontology.org/format_1915"
is_obsolete: true
[Term]
id: NFDI4PSO:0000022
name: Raw data file checksum
def: "Checksum of the raw data file, it is a specialised concept of http://purl.obolibrary.org/obo/NCIT_C43522” ! Checksum" []
is_obsolete: true
[Term]
id: NFDI4PSO:0000023
name: Data filtering software
def: "Name of the software applied for data filtering" []
comment: “For RNA-seq data, this may be a read adapter trimming software (GENEPIO_0002096)”
is_obsolete: true
[Term]
id: NFDI4PSO:0000024
name: Data filtering software version
def: "The version of the data filtering software (NFDI4PSO:0000023).”" []
comment: “”
is_obsolete: true
[Term]
id: NFDI4PSO:0000025
name: Data filtering Software Parameters
def: "The parameters of the data filtering software (NFDI4PSO:0000023).”" []
comment: “”
is_obsolete: true
[Term]
id: NFDI4PSO:0000026
name: Genome reference sequence
def: "Name and version of the genome reference.”" []
comment: “See also http://purl.obolibrary.org/obo/NCIT_C164388 and http://purl.obolibrary.org/obo/MS_1002644”
is_obsolete: true
[Term]
id: NFDI4PSO:0000027
name: Processed data file format
def: "File format of the processed data file”" []
comment: “”
is_obsolete: true
[Term]
id: NFDI4PSO:0000028
name: Processed data file name
def: "Name of the processed data file”" []
comment: “”
is_obsolete: true
[Term]
id: NFDI4PSO:0000029
name: Processed data file checksum
def: "Checksum of the processed data file, it is a specialised concept of http://purl.obolibrary.org/obo/NCIT_C43522” ! Checksum" []
is_obsolete: true
[Term]
id: NFDI4PSO:0000030
name: Organism
def: "A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs." []
xref: OBI:0100026
is_obsolete: true
[Term]
id: NFDI4PSO:0000031
name: Genotype
def: "The total sum of the genetic information of an organism that is known and relevant to the experiment being performed, including chromosomal, plasmid, viral or other genetic material which has been introduced into the organism either prior to or during the experiment." []
xref: EFO:0000513
is_obsolete: true
[Term]
id: NFDI4PSO:0000032
name: Organism part
def: "The part of organism's anatomy or substance arising from an organism from which the biomaterial was derived, excludes cells. E.g. tissue, organ, system, sperm, blood or body location (arm)." []
xref: EFO:0000635
is_obsolete: true
[Term]
id: NFDI4PSO:0000033
name: Plant age
def: "A temporal measurement of the time period elapsed since an identifiable point in the life cycle of an organism. If a developmental stage is specified, the identifiable point would be the beginning of that stage. Otherwise the identifiable point must be specified such as planting (e.g. 3 days post planting)." []
comment: “This is a specialization of http://www.ebi.ac.uk/efo/EFO_0000246"
is_obsolete: true
[Term]
id: NFDI4PSO:0000034
name: Time point
def: "Time point at which a sample or observation is made or taken from a biomaterial as measured from some reference point." []
xref: EFO:0000724
is_obsolete: true
[Term]
id: NFDI4PSO:0000035
name: Library strategy
def: "Sequencing technique intended for a next generation sequencing library." []
xref: GENEPIO:0001973
is_obsolete: true
[Term]
id: NFDI4PSO:0000036
name: Library Selection
def: "The method used to select for or against, enrich, or screen the material being sequenced." []
xref: GENEPIO:0001940
is_obsolete: true
[Term]
id: NFDI4PSO:0000037
name: Library preparation kit
def: "Packaged kits (containing adapters, indexes, enzymes, buffers etc), tailored for specific sequencing workflows, which allow the simplified preparation of sequencing-ready libraries for small genomes, amplicons, and plasmids." []
xref: GENEPIO:0000085
is_obsolete: true
[Term]
id: NFDI4PSO:0000038
name: Library preparation kit version
def: "The version identifier of a packaged kit tailored for specific sequencing workflows." []
xref: GENEPIO:0000149
is_obsolete: true
[Term]
id: NFDI4PSO:0000039
name: Adapter sequence
def: "Adapters provide priming sequences for both amplification and sequencing of the sample-library fragments. Both adapters should be reported; in uppercase letters." []
xref: GENEPIO:0000083
is_obsolete: true
[Term]
id: NFDI4PSO:0000040
name: Next generation sequencing instrument model
def: "Model name or number of next generation sequencing instrument" []
xref: EFO:0003739
is_obsolete: true
[Term]
id: NFDI4PSO:0000041
name: Growth day length
def: "The time (e.g. hours of light) of the light regime in a growth experiment (e.g. 12hr light /12hr dark, 12/12, short day, long day)" []
comment: “Adapted from 'light quantity exposure' http://purl.obolibrary.org/obo/PECO_0007078"
is_obsolete: true
[Term]
id: NFDI4PSO:0000042
name: Biological replicate
def: "Indicates the biological replication during experiment design (e.g. 'rep1', 'rep2')" []
comment: “Similar to http://purl.obolibrary.org/obo/MS_1001809"
is_obsolete: true
[Term]
id: NFDI4PSO:0000043
name: MS sample post-extraction
def: "Specific to metabolomic mass spectrometry assays. Steps performed after sample extraction (e.g. dried in a vacuum concentrator, solid phase microextraction direct injection)" []
comment: “"
is_obsolete: true
[Term]
id: NFDI4PSO:0000044
name: MS sample resuspension
def: "Specific to metabolomic mass spectrometry assays. Resuspension after sample extraction (e.g. dried samples resuspended in pyridine, dried samples resuspended in acetonitrile)" []
comment: “"
is_obsolete: true
[Term]
id: NFDI4PSO:0000045
name: MS sample type
def: "Specific to metabolomic mass spectrometry assays. Type of sample (e.g. experimental sample, pooled sample, blank, medium blank, retention index, reference standard, quality control)" []
comment: “"
is_obsolete: true
[Term]
id: NFDI4PSO:0000046
name: Chromatography instrument model
def: "Company name, and instrument name or serial number of the chromatography instrument" []
comment: is_a http://purl.obolibrary.org/obo/OBI_0000048
is_obsolete: true
[Term]
id: NFDI4PSO:0000047
name: Chromatography autosampler model
def: "Company name, and name or serial number of the chromatography autosampler model" []
comment: is_a http://purl.obolibrary.org/obo/OBI_0000555
is_obsolete: true
[Term]
id: NFDI4PSO:0000048
name: Chromatography column model
def: "Company name, and name or serial number of the chromatography column" []
is_obsolete: true
[Term]
id: NFDI4PSO:0000049
name: Chromatography guard column model
def: "Company name, and name or serial number of the chromatography guard column" []
comment: is_a http://purl.obolibrary.org/obo/OBI_0000614
is_obsolete: true
[Term]
id: NFDI4PSO:0000050
name: Extraction buffer
def: "Chemical buffer, solvent or solution used to extract a component from a biological sample." []
comment: “related to http://purl.obolibrary.org/obo/OBI_0302884. DB"
is_obsolete: true
[Term]
id: NFDI4PSO:0000051
name: Extraction buffer volume
def: "Volume of the buffer (NFDI4PSO:0000050) used during extraction." []
comment: related to http://purl.obolibrary.org/obo/OBI_0302884
is_obsolete: true
[Term]
id: NFDI4PSO:0000052
name: MS derivatization
def: "Derivatization for metabolomics mass spectrometry." []
xref: CHMO:0001485
is_obsolete: true
[Term]
id: NFDI4PSO:0000053
name: Chromatography column type
def: "Type of chromatography column (NFDI4PSO:0000048)" []
xref: CHMO:0001000
is_obsolete: true
[Term]
id: NFDI4PSO:0000054
name: Extraction method
def: "Method or kit that was used to extract DNA or RNA" []
comment: “More general than NFDI4PSO:0000014, because not everyone uses a kit for RNA/DNA extraction"
is_obsolete: true
[Term]
id: NFDI4PSO:0000055
name: Library source
def: "Type of source material that is being sequenced" []
xref: GENEPIO:0001965
is_obsolete: true
[Term]
id: NFDI4PSO:0000056
name: Library DNA amount
def: "Amount of DNA (microgram) used as starting material for library construction" []
comment: “"
is_obsolete: true
[Term]
id: NFDI4PSO:0000057
name: Next generation sequencing platform
def: "Name of the company that produces next generation sequencing instruments" []
xref: GENEPIO:0000071
is_obsolete: true
[Term]
id: NFDI4PSO:0000058
name: Read length
def: "Numbers of base pairs per read" []
xref: GENEPIO:0000076
is_obsolete: true
[Term]
id: NFDI4PSO:0000059
name: Sequence assembly method
def: "Strategy that was used to assemble reads into contigs" []
comment: “Just two options should be possible: de-novo assembly or mapping"
xref: GENEPIO:0000090
is_obsolete: true
[Term]
id: NFDI4PSO:0000060
name: Sequence assembly algorithm version
def: "The version of the sequence assembly algorithm (OBI_0001522)" []
comment: “"
is_obsolete: true
[Term]
id: NFDI4PSO:0000061
name: Genome status
def: "Status of the genome sequence that is uploaded" []
comment: “Just two options should be possible: full or partial"
is_obsolete: true
[Term]
id: NFDI4PSO:0000062
name: RNA quality check
def: "Measure of RNA quality after RNA extraction. Typically RNA integrity number (RIN) as provided by Agilent BioAnalyzer. Alternatively, RNA integrity checked via gel electrophoresis." []
is_obsolete: true
[Term]
id: NFDI4PSO:0000063
name: BioProject Accession Number
def: "The accession number of the BioProject(s) to which the BioSample belongs. If the BioSample belongs to more than one BioProject, enter multiple bioproject_accession columns. A valid BioProject accession has prefix PRJN, PRJE or PRJD, e.g., PRJNA12345." []
comment: “[Definition Source: taken from a template at https://www.ncbi.nlm.nih.gov/biosample/]"
xref: NCIT:C175890
is_obsolete: true
[Term]
id: NFDI4PSO:0000064
name: Sample type
def: "Sample type, such as cell culture, mixed culture, tissue sample, whole organism, single cell, metagenomic assembly" []
comment: “[Definition Source: taken from a template at https://www.ncbi.nlm.nih.gov/biosample/]"
xref: NCIT:C70713
is_obsolete: true
[Term]
id: NFDI4PSO:0000065
name: Isolate
def: "A specific individual microbe and its genetically identical progeny separated on a single occasion from a sample taken from a host or culture system. [Definition Source: NCI]" []
xref: NCIT:C53471
is_obsolete: true
[Term]
id: NFDI4PSO:0000066
name: Cultivar
def: "A cultivated plant variety selected and given a name because it has desirable characteristics that distinguish it from otherwise similar plants of the same species." []
comment: “[Definition Source: http://www.ebi.ac.uk/efo/EFO_0005136]"
xref: EFO:0005136
is_obsolete: true
[Term]
id: NFDI4PSO:0000067
name: Ecotype
def: "A biotype resulting from selection in a particular habitat, e.g. the A. thaliana Ecotype Ler" []
comment: “[Definition Source: http://www.ebi.ac.uk/efo/EFO_0000434]"
xref: EFO:0000434
is_obsolete: true
[Term]
id: NFDI4PSO:0000068
name: Cell line
def: "A permanently established cell culture that will proliferate indefinitely given appropriate fresh medium and space. [Definition Source: NCI][attribution: On-line Medical Dictionary]" []
comment: “[Definition Source: http://purl.obolibrary.org/obo/NCIT_C16403]"
xref: NCIT:C16403
is_obsolete: true
[Term]
id: NFDI4PSO:0000069
name: Cell type
def: "The smallest units of living structure capable of independent existence, composed of a membrane-enclosed mass of protoplasm and containing a nucleus or nucleoid. [Definition Source: NCI]" []
comment: “[Definition Source: http://purl.obolibrary.org/obo/NCIT_C12508]"
xref: NCIT:C12508
is_obsolete: true
[Term]
id: NFDI4PSO:0000070
name: Developmental Stage
def: "A general term that usually refers to named landmark events during development of an organism. [Definition Source: NCI]" []
comment: “[Definition Source: http://purl.obolibrary.org/obo/NCIT_C43531]"
xref: NCIT:C43531
is_obsolete: true
[Term]
id: NFDI4PSO:0000071
name: Plant disease
def: "A biotic plant stress caused by exposure to an environment containing a biological stress agent." []
comment: “[Definition Source: http://purl.obolibrary.org/obo/PSO_0000013]"
xref: PSO:0000013
[Term]
id: NFDI4PSO:0000072
name: Plant disease stage
def: "Stage of plant disease (NFDI4PSO:0000071) at the time of sampling." []
is_obsolete: true
[Term]
id: NFDI4PSO:0000073
name: Phenotype
def: "Phenotype of sampled organism. For Phenotypic quality Ontology (PATO) (v1.269) terms, please see http://bioportal.bioontology.org/visualize/44601" []
comment: “[Definition Source: taken from a template at https://www.ncbi.nlm.nih.gov/biosample/]"
xref: NCIT:C16977
is_obsolete: true
[Term]
id: NFDI4PSO:0000074
name: Geogaphic Area
def: "Geographical origin of the sample; use the appropriate name from this list http://www.insdc.org/documents/country-qualifier-vocabulary. Use a colon to separate the country or ocean from more detailed information about the location, eg 'Canada: Vancouver' or 'Germany: halfway down Zugspitze, Alps'" []
comment: “[Definition Source: taken from a template at https://www.ncbi.nlm.nih.gov/biosample/]"
xref: NCIT:C16632
is_obsolete: true
[Term]
id: NFDI4PSO:0000075
name: Sample Collection Date
def: "The date on which the sample was collected" []
xref: NCIT:C81286
is_obsolete: true
[Term]
id: NFDI4PSO:0000076
name: Sample Collected By
def: "Indicates the person, group, or institution who performed the collection act. [Definition Source: NCI]" []
comment: “[Definition Source: http://purl.obolibrary.org/obo/NCIT_C45262"
xref: NCIT:C45262
is_obsolete: true
[Term]
id: NFDI4PSO:0000077
name: Metabolite Assignment File
def: "metabolite assignment file (MAF) as required by MetaboLights to describe metabolites analyzed during a metabolomics assay. Details see: https://www.ebi.ac.uk/metabolights/guides/MAF/Title" []
comment: “[Definition Source: https://www.ebi.ac.uk/metabolights/guides/MAF/Title"
is_obsolete: true
[Term]
id: NFDI4PSO:0000078
name: BioSample Accession Number
def: "BioSample accession as required by NCBI repositories. Typically of the form SAMN[number]. NOT SUB[number]!" []
comment: “[Definition Source: taken from a template at https://www.ncbi.nlm.nih.gov/biosample/]"
xref: NCIT:C175889
is_obsolete: true
[Term]
id: NFDI4PSO:0000079
name: label
def: "A role played by a part of a molecular entity distinguishable by the observer but not by the system and used to identify a tracer." []
xref: CHEBI:35209
is_obsolete: true
[Term]
id: NFDI4PSO:0000080
name: mobile phase
def: "A fluid that percolates through or along the stationary bed in chromatography." []
xref: CHMO:0000995
is_obsolete: true
[Term]
id: NFDI4PSO:0000081
name: Chromatography gradient
def: "Settings of the gradient used during (e.g. liquid, gas or ion) chromatography" []
comment: "term was previously !elution!"
is_obsolete: true
[Term]
id: NFDI4PSO:0000082
name: rRNA depletion
def: "Method used for rRNA depletion during construction of the sequencing library." []
comment: "see also http://purl.obolibrary.org/obo/NCIT_C18685"
is_obsolete: true
[Term]
id: NFDI4PSO:0002000
name: alias
def: "Unique identificator for a study. This is used to link experiments to the study." []
is_obsolete: true
[Term]
id: NFDI4PSO:0002001
name: study_abstract
def: "Briefly describes the goals, purpose, and scope of the Study. This need not be listed if it can be inherited from a referenced publication." []
is_obsolete: true
[Term]
id: NFDI4PSO:0002002
name: title
def: "Title of the study as would be used in a publication." []
is_obsolete: true
[Term]
id: NFDI4PSO:0002003
name: latitude
def: "The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system." []
xref: SIO:000319
is_obsolete: true
[Term]
id: NFDI4PSO:0002004
name: longitude
def: "The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system." []
xref: SIO:000318
is_obsolete: true
[Term]
id: NFDI4PSO:0002005
name: project name
def: "Name of the project within which the experiment was organized." []
is_obsolete: true
[Term]
id: NFDI4PSO:0002006
name: sequencing method
def: "Sequencing method used; e.g. Sanger, pyrosequencing, ABI-solid." []
is_obsolete: true
[Term]
id: NFDI4PSO:0002007
name: investigation type
def: "Nucleic Acid Sequence Report is the root element of all MIxS compliant reports as standardized by Genomic Standards Consortium" []
is_obsolete: true
[Term]
id: NFDI4PSO:0002008
name: environment (feature)
def: "Environmental feature level includes geographic environmental features. Compared to biome, feature is a descriptor of the more local environment. Examples include: harbor, cliff, or lake. EnvO (v 2013-06-14) terms can be found via the link: www.environmentontology.org/Browse-EnvO" []
xref: ENVO:01000813
is_obsolete: true
[Term]
id: NFDI4PSO:0002009
name: environment (material)
def: "The environmental material level refers to the material that was displaced by the sample, or material in which a sample was embedded, prior to the sampling event. Environmental material terms are generally mass nouns. Examples include: air, soil, or water. EnvO (v 2013-06-14) terms can be found via the link: www.environmentontology.org/Browse-EnvO" []
xref: ENVO:00010483
is_obsolete: true
[Term]
id: NFDI4PSO:0002010
name: plant-associated environmental package
def: "MIGS/MIMS/MIMARKS extension for reporting of measurements and observations obtained from one or more of the environments where the sample was obtained. All environmental packages listed here are further defined in separate subtables. By giving the name of the environmental package, a selection of fields can be made from the subtables and can be reported" []
is_obsolete: true
[Term]
id: NFDI4PSO:0010000
name: ENA
def: "The European Nucleotide Archive (ENA) is an open, supported platform for the management, sharing, integration, archiving and dissemination of sequence data." []
comment: https://www.ebi.ac.uk/ena/
is_a: NFDI4PSO:1000095 ! Endpoint Repository
property_value: http://purl.org/dc/elements/1.1/creator http://orcid.org/0000-0001-9021-3197
property_value: http://purl.org/dc/elements/1.1/date 2022-02-02T08:33:08Z xsd:dateTime
created_by: Dominik Brilhaus
is_obsolete: true
[Term]
id: NFDI4PSO:0010002
name: BIOSAMPLE
def: "The BioSample database contains descriptions of biological source materials used in experimental assays." []
comment: https://www.ncbi.nlm.nih.gov/biosample/
is_a: NFDI4PSO:1000095 ! Endpoint Repository
property_value: http://purl.org/dc/elements/1.1/creator http://orcid.org/0000-0001-9021-3197
property_value: http://purl.org/dc/elements/1.1/date 2022-02-02T08:33:08Z xsd:dateTime
created_by: Dominik Brilhaus
is_obsolete: true
[Term]
id: NFDI4PSO:0010004
name: BIOPROJECT
def: "A BioProject is a collection of biological data related to a single initiative, originating from a single organization or from a consortium. A BioProject record provides users a single place to find links to the diverse data types generated for that project." []
comment: https://www.ncbi.nlm.nih.gov/bioproject/
is_a: NFDI4PSO:1000095 ! Endpoint Repository
property_value: http://purl.org/dc/elements/1.1/creator http://orcid.org/0000-0001-9021-3197
property_value: http://purl.org/dc/elements/1.1/date 2022-02-02T08:58:37Z xsd:dateTime
created_by: Dominik Brilhaus
is_obsolete: true
[Term]
id: NFDI4PSO:0010005
name: GENBANK
def: "GenBank is the NIH genetic sequence database, an annotated collection of all publicly available DNA sequences (Nucleic Acids Research, 2013 Jan;41(D1):D36-42). GenBank is part of the International Nucleotide Sequence Database Collaboration, which comprises the DNA DataBank of Japan (DDBJ), the European Nucleotide Archive (ENA), and GenBank at NCBI. These three organizations exchange data on a daily basis." []
comment: https://www.ncbi.nlm.nih.gov/genbank/
is_a: NFDI4PSO:1000095 ! Endpoint Repository
property_value: http://purl.org/dc/elements/1.1/creator http://orcid.org/0000-0001-9021-3197
property_value: http://purl.org/dc/elements/1.1/date 2022-02-02T08:59:49Z xsd:dateTime
created_by: Dominik Brilhaus
is_obsolete: true
[Term]
id: NFDI4PSO:0010006
name: SRA
def: "Sequence Read Archive (SRA) data, available through multiple cloud providers and NCBI servers, is the largest publicly available repository of high throughput sequencing data. The archive accepts data from all branches of life as well as metagenomic and environmental surveys. SRA stores raw sequencing data and alignment information to enhance reproducibility and facilitate new discoveries through data analysis." []
comment: https://www.ncbi.nlm.nih.gov/sra/
is_a: NFDI4PSO:1000095 ! Endpoint Repository
property_value: http://purl.org/dc/elements/1.1/creator http://orcid.org/0000-0001-9021-3197
property_value: http://purl.org/dc/elements/1.1/date 2022-02-02T09:02:27Z xsd:dateTime
created_by: Dominik Brilhaus
is_obsolete: true
[Term]
id: NFDI4PSO:0010007
name: PGP
def: "Plant Genomics & Phenomics Research Data Repository" []
comment: https://edal-pgp.ipk-gatersleben.de
is_a: NFDI4PSO:1000095 ! Endpoint Repository
property_value: http://purl.org/dc/elements/1.1/creator http://orcid.org/0000-0001-9021-3197
property_value: http://purl.org/dc/elements/1.1/date 2022-02-02T09:03:35Z xsd:dateTime
created_by: Dominik Brilhaus
is_obsolete: true
[Term]
id: NFDI4PSO:0010008
name: BIA
def: "The BioImage Archive (BIA) stores and distributes biological images that are useful to life sciences researchers. It also provides data archiving services to the broader bioimaging database community including added-value bioimaging data resources such as EMPIAR, Cell-IDR and Tissue-IDR." []
comment: https://www.ebi.ac.uk/bioimage-archive/
is_a: NFDI4PSO:1000095 ! Endpoint Repository
property_value: http://purl.org/dc/elements/1.1/creator http://orcid.org/0000-0001-9021-3197
property_value: http://purl.org/dc/elements/1.1/date 2022-02-02T09:04:46Z xsd:dateTime
created_by: Dominik Brilhaus[Term]
is_obsolete: true
[Term]
id: NFDI4PSO:0010009
name: Biosource material state
def: "The state (typically fresh or dry) of the biosource material (e.g. tissue) prepared for an assay." []
comment: "Relates to NFDI4PSO:0000013 ! Biosource amount"
property_value: http://purl.org/dc/elements/1.1/creator http://orcid.org/0000-0001-9021-3197
created_by: Dominik Brilhaus
is_obsolete: true
[Term]
id: NFDI4PSO:0010010
name: Fresh material
def: "Fresh (non-dry) biosource material" []
comment: "Relates to https://cropontology.org/rdf/CO_347:0000193 ! Plant FW - Measurement"
is_a: NFDI4PSO:0010009
property_value: http://purl.org/dc/elements/1.1/creator http://orcid.org/0000-0001-9021-3197
created_by: Dominik Brilhaus
is_obsolete: true
[Term]
id: NFDI4PSO:0010011
name: Dry material
def: "Dry biosource material" []
comment: "Relates to https://cropontology.org/rdf/CO_347:0000196 ! Plant DW - Measurement"
is_a: NFDI4PSO:0010009
property_value: http://purl.org/dc/elements/1.1/creator http://orcid.org/0000-0001-9021-3197
created_by: Dominik Brilhaus
is_obsolete: true
[Term]
id: NFDI4PSO:0010012
name: Internal standard
def: "Internal standard added in known amount to an analytical sample" []
comment: "Similar to http://purl.obolibrary.org/obo/MSIO_0000005 ! internal standard role"
property_value: http://purl.org/dc/elements/1.1/creator http://orcid.org/0000-0001-9021-3197
created_by: Dominik Brilhaus
is_obsolete: true
[Term]
id: NFDI4PSO:0010013
name: Sample volume
def: "Volume taken from the sample to be assayed (measured)." []
property_value: http://purl.org/dc/elements/1.1/creator http://orcid.org/0000-0001-9021-3197
created_by: Dominik Brilhaus
is_obsolete: true
[Term]
id: NFDI4PSO:0010014
name: Chromatography injection volume
def: "Volume of the sample injected during chromatography" []
comment: "Relates to http://purl.allotrope.org/ontologies/result#AFR_0001577 ! injection volume setting"
property_value: http://purl.org/dc/elements/1.1/creator http://orcid.org/0000-0001-9021-3197
created_by: Dominik Brilhaus
is_obsolete: true
[Term]
id: NFDI4PSO:0010015
name: Chromatography injection mode
def: "This is to specify split / splitless runs during e.g. gas-chromatography." []
comment: "Compare to http://purl.obolibrary.org/obo/OBI_0000525 ! splitless GC injector"
property_value: http://purl.org/dc/elements/1.1/creator http://orcid.org/0000-0001-9021-3197
created_by: Dominik Brilhaus
is_obsolete: true
[Term]
id: NFDI4PSO:1000000
name: _NotUse_TemplateTerm
def: "This is a helper term, since I was unable to properly handle custom `property_value` tags with Protege... Dominik" []
comment: "For property values that are not ontology terms themselves, but literals/strings, add `xsd:string`"
property_value: ER_target NFDI4PSO:1000099
property_value: ER_target "Put name of ER here" xsd:string
property_value: ER_target_term "Put name of ER target term for which this term should be selectable" xsd:string
property_value: UserInstruction "This could be a place for detailed user instructions in SWATE templates" xsd:string
is_obsolete: true
[Term]
id: NFDI4PSO:1000003
name: RNA-Seq
def: "placeholder def of RNA-Seq" []
comment: To be transformed to an instance. DB
is_a: NFDI4PSO:0000035 ! Library strategy
property_value: ER_target "GEO_RNASEQ" xsd:string
property_value: ER_target_term "PROTOCOLS_library strategy" xsd:string
is_obsolete: true
[Term]
id: NFDI4PSO:1000004
name: miRNA-Seq
def: "placeholder def of miRNA-Seq" []
comment: To be transformed to an instance. DB
is_a: NFDI4PSO:0000035 ! Library strategy
property_value: ER_target "GEO_RNASEQ" xsd:string
property_value: ER_target_term "PROTOCOLS_library strategy" xsd:string
is_obsolete: true
[Term]
id: NFDI4PSO:1000005
name: ncRNA-Seq
def: "placeholder def of ncRNA-Seq" []
comment: To be transformed to an instance. DB
is_a: NFDI4PSO:0000035 ! Library strategy
property_value: ER_target "GEO_RNASEQ" xsd:string
property_value: ER_target_term "PROTOCOLS_library strategy" xsd:string
is_obsolete: true
[Term]
id: NFDI4PSO:1000006
name: RNA-Seq (size fractionation)
def: "placeholder def of RNA-Seq (size fractionation)" []
comment: To be transformed to an instance. DB
is_a: NFDI4PSO:0000035 ! Library strategy
property_value: ER_target "GEO_RNASEQ" xsd:string
property_value: ER_target_term "PROTOCOLS_library strategy" xsd:string
is_obsolete: true
[Term]
id: NFDI4PSO:1000007
name: RNA-Seq (CAGE)
def: "placeholder def of RNA-Seq (CAGE)" []
comment: To be transformed to an instance. DB
is_a: NFDI4PSO:0000035 ! Library strategy
property_value: ER_target "GEO_RNASEQ" xsd:string
property_value: ER_target_term "PROTOCOLS_library strategy" xsd:string
is_obsolete: true
[Term]
id: NFDI4PSO:1000008
name: RNA-Seq (RACE)
def: "placeholder def of RNA-Seq (RACE)" []
comment: To be transformed to an instance. DB
is_a: NFDI4PSO:0000035 ! Library strategy
property_value: ER_target "GEO_RNASEQ" xsd:string
property_value: ER_target_term "PROTOCOLS_library strategy" xsd:string
is_obsolete: true
[Term]
id: NFDI4PSO:1000009
name: ssRNA-seq
def: "placeholder def of ssRNA-seq" []
comment: To be transformed to an instance. DB
is_a: NFDI4PSO:0000035 ! Library strategy
property_value: ER_target "GEO_RNASEQ" xsd:string
property_value: ER_target_term "PROTOCOLS_library strategy" xsd:string
is_obsolete: true
[Term]
id: NFDI4PSO:1000010
name: ChIP-Seq
def: "placeholder def of ChIP-Seq" []
comment: To be transformed to an instance. DB
is_a: NFDI4PSO:0000035 ! Library strategy
property_value: ER_target "GEO_RNASEQ" xsd:string
property_value: ER_target_term "PROTOCOLS_library strategy" xsd:string
is_obsolete: true
[Term]
id: NFDI4PSO:1000011
name: MNase-Seq
def: "placeholder def of MNase-Seq" []
comment: To be transformed to an instance. DB
is_a: NFDI4PSO:0000035 ! Library strategy
property_value: ER_target "GEO_RNASEQ" xsd:string
property_value: ER_target_term "PROTOCOLS_library strategy" xsd:string
is_obsolete: true
[Term]
id: NFDI4PSO:1000012
name: MBD-Seq
def: "placeholder def of MBD-Seq" []
comment: To be transformed to an instance. DB
is_a: NFDI4PSO:0000035 ! Library strategy
property_value: ER_target "GEO_RNASEQ" xsd:string
property_value: ER_target_term "PROTOCOLS_library strategy" xsd:string
is_obsolete: true
[Term]
id: NFDI4PSO:1000013
name: MRE-Seq
def: "placeholder def of MRE-Seq" []
comment: To be transformed to an instance. DB
is_a: NFDI4PSO:0000035 ! Library strategy
property_value: ER_target "GEO_RNASEQ" xsd:string
property_value: ER_target_term "PROTOCOLS_library strategy" xsd:string
is_obsolete: true
[Term]
id: NFDI4PSO:1000014
name: Bisulfite-Seq
def: "placeholder def of Bisulfite-Seq" []
comment: To be transformed to an instance. DB
is_a: NFDI4PSO:0000035 ! Library strategy
property_value: ER_target "GEO_RNASEQ" xsd:string
property_value: ER_target_term "PROTOCOLS_library strategy" xsd:string
is_obsolete: true
[Term]
id: NFDI4PSO:1000015
name: Bisulfite-Seq (reduced representation)
def: "placeholder def of Bisulfite-Seq (reduced representation)" []
comment: To be transformed to an instance. DB
is_a: NFDI4PSO:0000035 ! Library strategy
property_value: ER_target "GEO_RNASEQ" xsd:string
property_value: ER_target_term "PROTOCOLS_library strategy" xsd:string
is_obsolete: true
[Term]
id: NFDI4PSO:1000016
name: MeDIP-Seq
def: "placeholder def of MeDIP-Seq" []
comment: To be transformed to an instance. DB
is_a: NFDI4PSO:0000035 ! Library strategy
property_value: ER_target "GEO_RNASEQ" xsd:string
property_value: ER_target_term "PROTOCOLS_library strategy" xsd:string
is_obsolete: true
[Term]
id: NFDI4PSO:1000017
name: DNase-Hypersensitivity
def: "placeholder def of DNase-Hypersensitivity" []
comment: To be transformed to an instance. DB
is_a: NFDI4PSO:0000035 ! Library strategy
property_value: ER_target "GEO_RNASEQ" xsd:string
property_value: ER_target_term "PROTOCOLS_library strategy" xsd:string
is_obsolete: true
[Term]
id: NFDI4PSO:1000018
name: Tn-Seq
def: "placeholder def of Tn-Seq" []
comment: To be transformed to an instance. DB
is_a: NFDI4PSO:0000035 ! Library strategy
property_value: ER_target "GEO_RNASEQ" xsd:string
property_value: ER_target_term "PROTOCOLS_library strategy" xsd:string
is_obsolete: true
[Term]
id: NFDI4PSO:1000019
name: FAIRE-seq
def: "placeholder def of FAIRE-seq" []
comment: To be transformed to an instance. DB
is_a: NFDI4PSO:0000035 ! Library strategy
property_value: ER_target "GEO_RNASEQ" xsd:string